[CHNOSZ-commits] r299 - in pkg/CHNOSZ: . R data inst inst/extdata/Berman inst/extdata/Berman/unused inst/extdata/OBIGT tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 13 07:42:35 CET 2017
Author: jedick
Date: 2017-12-13 07:42:35 +0100 (Wed, 13 Dec 2017)
New Revision: 299
Added:
pkg/CHNOSZ/inst/extdata/Berman/unused/
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.bib
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_refs.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
Removed:
pkg/CHNOSZ/inst/extdata/Berman/BA96.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/data/OBIGT.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/data/thermo.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/vignettes/obigt.bib
Log:
move BA96.csv to extdata/Berman/unused/BA96.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/DESCRIPTION 2017-12-13 06:42:35 UTC (rev 299)
@@ -1,6 +1,6 @@
Date: 2017-12-13
Package: CHNOSZ
-Version: 1.1.3-5
+Version: 1.1.3-6
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/R/berman.R 2017-12-13 06:42:35 UTC (rev 299)
@@ -19,12 +19,11 @@
SHD91 <- read.csv(paste0(dir, "/SHD91.csv"), as.is=TRUE)
ZS92 <- read.csv(paste0(dir, "/ZS92.csv"), as.is=TRUE)
JUN92 <- read.csv(paste0(dir, "/JUN92.csv"), as.is=TRUE)
- BA96 <- read.csv(paste0(dir, "/BA96.csv"), as.is=TRUE)
DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
# assemble the files in reverse chronological order
- dat <- rbind(BDat17, FDM14, DS10, BA96, JUN92, ZS92, SHD91, Ber90, Ber88)
+ dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
# remove duplicates (only the first, i.e. most recent entry is kept)
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers
Modified: pkg/CHNOSZ/data/OBIGT.R
===================================================================
--- pkg/CHNOSZ/data/OBIGT.R 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/data/OBIGT.R 2017-12-13 06:42:35 UTC (rev 299)
@@ -12,9 +12,11 @@
sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
sources_liq <- paste0(c("organic"), "_liq")
sources_gas <- paste0(c("inorganic", "organic"), "_gas")
+ sources <- c(sources_aq, sources_cr, sources_liq, sources_gas)
OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ")
# need explicit "/" for Windows
- sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv.xz")
+ sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv")
+ sourcefiles[!sources=="Berman_cr"] <- paste0(sourcefiles[!sources=="Berman_cr"], ".xz")
datalist <- lapply(sourcefiles, read.csv, as.is=TRUE)
obigt <- do.call(rbind, datalist)
# get thermo from CHNOSZ environment
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/data/refs.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -49,11 +49,6 @@
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes not included in later slop files.",https://doi.org/10.1016/0016-7037(95)00058-8
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
-BA96,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","added minerals: Fe-cordierite, geikelite, hercynite, iron-a, iron-g, orthocorundum",https://doi.org/10.1007/s004100050233
-BA96.1,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp + V coefficients: almandine, anthyophyllite, fayalite, ferrosilite",https://doi.org/10.1007/s004100050233
-BA96.2,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H and S: cordierite, enstatite, hematite, magnetite, rutile",https://doi.org/10.1007/s004100050233
-BA96.3,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp coefficients: forsterite, pyrope, spinel",https://doi.org/10.1007/s004100050233
-BA96.4,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and V coefficients: ilmenite, talc",https://doi.org/10.1007/s004100050233
DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,http://dx.doi.org/10.1016/0016-7037(95)00403-3
AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
Modified: pkg/CHNOSZ/data/thermo.R
===================================================================
--- pkg/CHNOSZ/data/thermo.R 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/data/thermo.R 2017-12-13 06:42:35 UTC (rev 299)
@@ -13,9 +13,11 @@
sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
sources_liq <- paste0(c("organic"), "_liq")
sources_gas <- paste0(c("inorganic", "organic"), "_gas")
+ sources <- c(sources_aq, sources_cr, sources_liq, sources_gas)
OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ")
# need explicit "/" for Windows
- sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv.xz")
+ sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv")
+ sourcefiles[!sources=="Berman_cr"] <- paste0(sourcefiles[!sources=="Berman_cr"], ".xz")
datalist <- lapply(sourcefiles, read.csv, as.is=TRUE)
obigt <- do.call(rbind, datalist)
# create thermo list
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/inst/NEWS 2017-12-13 06:42:35 UTC (rev 299)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-5 (2017-12-13)
+CHANGES IN CHNOSZ 1.1.3-6 (2017-12-13)
--------------------------------------
- Lines in 1-D diagram()s can optionally be drawn as splines using the
@@ -11,7 +11,7 @@
- Add 'srt' argument to diagram() (rotation of line labels).
- Add mineral data from Berman and Aranovich, 1996 to
- extdata/Berman/BA96.csv.
+ extdata/Berman/unused/BA96.csv.
- Correct swapped v1 <-> v3 and v2 <-> v4 in extdata/Berman/DS10.csv.
Deleted: pkg/CHNOSZ/inst/extdata/Berman/BA96.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BA96.csv 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/inst/extdata/Berman/BA96.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -1,21 +0,0 @@
-name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
-almandine,,-5265440,341.51,11.529,621.43,-32.879,-150.81,221.187,-0.57,0.434,18.599,74.711,,,,,,,,,,,,,,
-anthophyllite,,-12074470,537.4,26.33,1233.79,-71.34,-221.638,233.394,-1.139,0,28.105,62.894,,,,,,,,,,,,,,
-cordierite,,-9161480,416.23,23.311,954.39,-79.623,-23.173,-37.021,-1.158,0,3.003,18.017,,,,,,,,,,,,,,
-Fe-cordierite,,-8430550,482.18,23.706,983.48,-84.037,-18.703,-8.568,-1.7,0,4.265,0,,,,,,,,,,,,,,
-fayalite,,-1477170,151.73,4.639,252,-20.137,0,-6.219,-0.822,1.944,26.21,84.233,,,,,,,,,,,,,,
-ferrosilite,,-1192910,96.47,3.295,174.2,-13.93,-4.544,-3.771,-0.911,0.303,31.406,80.4,,,,,,,,,,,,,,
-forsterite,,-2174420,94.18,4.36,233.18,-18.016,0,-26.794,-0.791,1.351,29.464,88.633,,,,,,,,,,,,,,
-geikelite,,-1570520,74.41,3.077,146.2,-4.16,-39.998,40.233,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
-hematite,,-826740,87.36,3.027,146.86,0,-55.768,52.563,-0.479,0.304,38.31,1.65,955,298,0,-7.403,27.921,1287,,,,,,,,
-hercynite,,-1945360,123.13,4.08,251.77,-20.444,-13.483,13.15,-0.51,0,15.819,96.276,,,,,,,,,,,,,,
-ilmenite,,-1233320,108.5,3.17,150,-4.416,-33.237,34.815,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
-iron-a,,0,27.45,0.709,51.87,-3.794,-25.43,50.68,-0.602,0,45.071,14.104,1042,298,-0.00057,-22.208,34.823,1000,,,,,,,,
-iron-g,,7720,35.64,0.691,66.24,-12.371,63.733,-106.04,-0.467,-1.445,47.153,14.451,,,,,,,,,,,,,,
-magnetite,,-1116960,146.04,4.452,207.93,0,-72.433,66.436,-0.582,1.751,30.291,138.47,848,298,0,-19.502,61.037,1565,,,,,,,,
-enstatite,,-1546040,66.18,3.133,166.58,-12.006,-22.706,27.915,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
-orthocorundum,,-1634950,33.93,3.123,119.38,7.748,-65.091,42.288,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
-pyrope,,-6284740,268.8,11.311,590.9,-28.27,-133.208,126.033,-0.576,0.442,22.519,37.044,,,,,,,,,,,,,,
-rutile,,-944750,50.88,1.883,77.84,0,-33.678,40.294,-0.454,0.585,25.716,15.409,,,,,,,,,,,,,,
-spinel,,-2302160,80.37,3.978,244.67,-20.04,,,-0.489,0,21.691,50.528,,,,,,,,,,,,,,
-talc,,-5898960,261.21,13.61,664.11,-51.872,-21.472,-32.737,-1.847,5.878,25.616,0,,,,,,,,,,,,,,
Added: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.bib
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.bib (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.bib 2017-12-13 06:42:35 UTC (rev 299)
@@ -0,0 +1,12 @@
+ at Article{BA96,
+ author = {Berman, R. G. and Aranovich, L. {\relax Ya}.},
+ journal = {Contributions to Mineralogy and Petrology},
+ title = {{O}ptimized standard state and solution properties of minerals. {I}. {M}odel calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system {F}e{O}-{M}g{O}-{C}a{O}-{A}l$_2${O}$_3$-{T}i{O}$_2$-{S}i{O}$2$},
+ year = {1996},
+ volume = {126},
+ number = {1},
+ pages = {25--37},
+ day = {01},
+ doi = {10.1007/s004100050233},
+ issn = {1432-0967},
+}
Copied: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv (from rev 298, pkg/CHNOSZ/inst/extdata/Berman/BA96.csv)
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -0,0 +1,21 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+almandine,,-5265440,341.51,11.529,621.43,-32.879,-150.81,221.187,-0.57,0.434,18.599,74.711,,,,,,,,,,,,,,
+anthophyllite,,-12074470,537.4,26.33,1233.79,-71.34,-221.638,233.394,-1.139,0,28.105,62.894,,,,,,,,,,,,,,
+cordierite,,-9161480,416.23,23.311,954.39,-79.623,-23.173,-37.021,-1.158,0,3.003,18.017,,,,,,,,,,,,,,
+Fe-cordierite,,-8430550,482.18,23.706,983.48,-84.037,-18.703,-8.568,-1.7,0,4.265,0,,,,,,,,,,,,,,
+fayalite,,-1477170,151.73,4.639,252,-20.137,0,-6.219,-0.822,1.944,26.21,84.233,,,,,,,,,,,,,,
+ferrosilite,,-1192910,96.47,3.295,174.2,-13.93,-4.544,-3.771,-0.911,0.303,31.406,80.4,,,,,,,,,,,,,,
+forsterite,,-2174420,94.18,4.36,233.18,-18.016,0,-26.794,-0.791,1.351,29.464,88.633,,,,,,,,,,,,,,
+geikelite,,-1570520,74.41,3.077,146.2,-4.16,-39.998,40.233,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
+hematite,,-826740,87.36,3.027,146.86,0,-55.768,52.563,-0.479,0.304,38.31,1.65,955,298,0,-7.403,27.921,1287,,,,,,,,
+hercynite,,-1945360,123.13,4.08,251.77,-20.444,-13.483,13.15,-0.51,0,15.819,96.276,,,,,,,,,,,,,,
+ilmenite,,-1233320,108.5,3.17,150,-4.416,-33.237,34.815,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
+iron-a,,0,27.45,0.709,51.87,-3.794,-25.43,50.68,-0.602,0,45.071,14.104,1042,298,-0.00057,-22.208,34.823,1000,,,,,,,,
+iron-g,,7720,35.64,0.691,66.24,-12.371,63.733,-106.04,-0.467,-1.445,47.153,14.451,,,,,,,,,,,,,,
+magnetite,,-1116960,146.04,4.452,207.93,0,-72.433,66.436,-0.582,1.751,30.291,138.47,848,298,0,-19.502,61.037,1565,,,,,,,,
+enstatite,,-1546040,66.18,3.133,166.58,-12.006,-22.706,27.915,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
+orthocorundum,,-1634950,33.93,3.123,119.38,7.748,-65.091,42.288,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
+pyrope,,-6284740,268.8,11.311,590.9,-28.27,-133.208,126.033,-0.576,0.442,22.519,37.044,,,,,,,,,,,,,,
+rutile,,-944750,50.88,1.883,77.84,0,-33.678,40.294,-0.454,0.585,25.716,15.409,,,,,,,,,,,,,,
+spinel,,-2302160,80.37,3.978,244.67,-20.04,,,-0.489,0,21.691,50.528,,,,,,,,,,,,,,
+talc,,-5898960,261.21,13.61,664.11,-51.872,-21.472,-32.737,-1.847,5.878,25.616,0,,,,,,,,,,,,,,
Added: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_obigt.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -0,0 +1,21 @@
+name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+almandine,Alm,Si3Fe3Al2O12,cr_Berman,BA96.1,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr_Berman,BA96.1,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,BA96.4,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr_Berman,Ber88,BA96.2,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr_Berman,Ber88,BA96.3,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,BA96.4,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-cordierite,fCd,Fe2Al4Si5O18,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+geikelite,Gk,MgTiO3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hercynite,Hc,FeAl2O4,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-a,aFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-g,gFe,Fe,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orthocorundum,Ok,Al2O3,cr_Berman,BA96,NA,12.Dec.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Added: pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_refs.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/unused/BA96_refs.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -0,0 +1,6 @@
+key,author,year,citation,note,URL
+BA96,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","added minerals: Fe-cordierite, geikelite, hercynite, iron-a, iron-g, orthocorundum",https://doi.org/10.1007/s004100050233
+BA96.1,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp + V coefficients: almandine, anthyophyllite, fayalite, ferrosilite",https://doi.org/10.1007/s004100050233
+BA96.2,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H and S: cordierite, enstatite, hematite, magnetite, rutile",https://doi.org/10.1007/s004100050233
+BA96.3,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp coefficients: forsterite, pyrope, spinel",https://doi.org/10.1007/s004100050233
+BA96.4,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and V coefficients: ilmenite, talc",https://doi.org/10.1007/s004100050233
Added: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2017-12-13 06:42:35 UTC (rev 299)
@@ -0,0 +1,87 @@
+name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+akermanite,Ak,Ca2MgSi2O7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+albite,Ab,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,high",hAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"albite,low",lAb,NaAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+almandine,Alm,Si3Fe3Al2O12,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+andalusite,And,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anorthite,An,Al2CaSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+antigorite,Atg,Mg48Si34O99H62O48,cr_Berman,Ber88,BDat17.1,09.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+brucite,Br,MgO2H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Ca-Al-pyroxene,CTs,CaAl2SiO6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+calcite,Cc,CaCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chrysotile,Chr,Mg3Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+clinochlore,Chl,Mg5Al2Si3O18H8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+coesite,Cs,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+corundum,Co,Al2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"cristobalite,alpha",aCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"cristobalite,beta",bCr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+diaspore,Dsp,AlO2H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+diopside,Di,MgCaSi2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+dolomite,Do,MgCaC2O6,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"enstatite,clino",cEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"enstatite,proto",pEn,MgSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+gehlenite,Ge,Al2Ca2SiO7,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+grossular,Gr,Ca3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr_Berman,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+jadeite,Jd,NaAlSi2O6,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+kaolinite,Kln,Al2Si2O9H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+kyanite,Ky,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+lawsonite,Lw,CaAl2Si2O10H4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+lime,Lm,CaO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnesite,Mst,MgCO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+margarite,Mrg,CaAl4Si2O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+meionite,Me,Ca4Al6Si6O27C,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+merwinite,Mw,Ca3MgSi2O8,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+monticellite,Mo,CaMgSiO4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+muscovite,Ms,KAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+paragonite,Pg,NaAl3Si3O12H2,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+periclase,Pe,MgO,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+phlogopite,Phl,KMg3AlSi3O12H2,cr_Berman,Ber88,SHD91.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+K-feldspar,Kfs,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"K-feldspar,high",Sa,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"K-feldspar,low",Mcr,KAlSi3O8,cr_Berman,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+prehnite,Prh,Ca2Al2Si3O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrophyllite,Prl,Al2Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+quartz,aQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"quartz,beta",bQz,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+sillimanite,Si,Al2SiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+sphene,Sph,CaTiSiO5,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+tremolite,Tr,Ca2Mg5Si8O24H2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"tridymite,high",hTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"tridymite,low",lTr,SiO2,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+wollastonite,Wo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pseudowollastonite,pWo,CaSiO3,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+zoisite,Zo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+clinozoisite,cZo,Ca2Al3Si3O13H,cr_Berman,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+annite,Ann,Si3Fe3AlKH2O12,cr_Berman,Ber90,SHD91.2,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluormuscovite,Flms,KAl3Si3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluorphlogopite,Fphl,KMg3AlSi3O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluorannite,Flan,Si3Fe3AlKO10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluortremolite,Fltr,Ca2Mg5Si8O22F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluorapatite,Flap,Ca5P3O12F,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hydroxyapatite,Hyap,Ca5P3O13H,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chlorapatite,Clap,Ca5P3O12Cl,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fluortalc,Fltc,Mg3Si4O10F2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chlorphlogopite,Cphl,KMg3AlSi3O10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+chlorannite,Clan,Si3Fe3AlKO10Cl2,cr_Berman,ZS92,NA,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+glaucophane,Glc,Na2Al2Mg3Si8O24H2,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pumpellyite,Pmp,Ca4Al5MgSi6O28H7,cr_Berman,Eva90,JUN92,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+aragonite,Arg,CaCO3,cr_Berman,FDM+14.1,NA,08.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hedenbergite,Hd,CaFeSi2O6,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+andradite,Adr,Ca3Fe2Si3O12,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferro-actinolite,Fac,Ca2Fe5Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+grunerite,Gru,Fe7Si8O22(OH)2,cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilvaite,Ilv,CaFe2FeSi2O7O(OH),cr_Berman,DS10,NA,08.Nov.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/tests/testthat/test-berman.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-berman.R 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/tests/testthat/test-berman.R 2017-12-13 06:42:35 UTC (rev 299)
@@ -32,13 +32,12 @@
# which minerals differ in DGf by more than 4 kcal/mol?
idiffG <- which(abs(prop_Berman$G - prop_Helgeson$G) > 4000)
expect_match(mineral[idiffG],
- "paragonite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite")
+ "paragonite|anthophyllite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite")
# which minerals differ in DHf by more than 4 kcal/mol?
idiffH <- which(abs(prop_Berman$H - prop_Helgeson$H) > 4000)
- # we get the above, plus phlogopite and clinozoisite:
expect_match(mineral[idiffH],
- "paragonite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite|clinozoisite")
+ "paragonite|anthophyllite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite|clinozoisite")
# which minerals differ in S by more than 4 cal/K/mol?
idiffS <- which(abs(prop_Berman$S - prop_Helgeson$S) > 4)
@@ -46,7 +45,7 @@
# which minerals differ in Cp by more than 4 cal/K/mol?
idiffCp <- which(abs(prop_Berman$Cp - prop_Helgeson$Cp) > 4)
- expect_match(mineral[idiffCp], "glaucophane|antigorite|cristobalite,beta|K-feldspar|fluortremolite|grunerite|almandine")
+ expect_match(mineral[idiffCp], "glaucophane|antigorite|cristobalite,beta|K-feldspar|fluortremolite|grunerite")
# which minerals differ in V by more than 1 cm^3/mol?
idiffV <- which(abs(prop_Berman$V - prop_Helgeson$V) > 1)
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2017-12-13 05:42:11 UTC (rev 298)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2017-12-13 06:42:35 UTC (rev 299)
@@ -1225,16 +1225,3 @@
url = {http://www.ingentaconnect.com/content/10.1127/0935-1221/2010/0022-2021},
}
- at Article{BA96,
- author = {Berman, R. G. and Aranovich, L. {\relax Ya}.},
- journal = {Contributions to Mineralogy and Petrology},
- title = {{O}ptimized standard state and solution properties of minerals. {I}. {M}odel calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system {F}e{O}-{M}g{O}-{C}a{O}-{A}l$_2${O}$_3$-{T}i{O}$_2$-{S}i{O}$2$},
- year = {1996},
- volume = {126},
- number = {1},
- pages = {25--37},
- day = {01},
- doi = {10.1007/s004100050233},
- issn = {1432-0967},
-}
-
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